Merge branch 'main' into simon-ra-variability-fig

naobservatory · Nov 28, 2023 · 121f272 · 121f272
2 parents f00ff05 + 66c052c
commit 121f272
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Showing 5 changed files with 2,208 additions and 2,203 deletions.
diff --git a/figures/counts-by-pathogen-and-study.py b/figures/counts-by-pathogen-and-study.py
@@ -14,8 +14,9 @@
 
 
 def start():
-    mgs_data = mgs.MGSData.from_repo()
-
+    branch = "simon-validation-exclusion-run"
+    # ref = "ref"
+    mgs_data = mgs.MGSData.from_repo(ref=branch)
     pathogen_taxids_by_name = defaultdict(list)
     for (
         pathogen_name,
@@ -150,7 +151,8 @@ def start():
         cellLoc="center",
         loc="upper left",
     )
-    fig.savefig("matching-reads-table.png", dpi=180)
+    fig.show()
+    fig.savefig(f"matching-reads-table_from{branch}.png", dpi=180)
     plt.clf()
 
 

diff --git a/fit.py b/fit.py
@@ -22,10 +22,12 @@ def summarize_output(coeffs: pd.DataFrame) -> pd.DataFrame:
 
 
 def start(num_samples: int, plot: bool) -> None:
+    branch = "simon-validation-exclusion-run"
+    print("Using mgs-pipeline branch simon-validation-exclusion-run")
     figdir = Path("fig")
     if plot:
         figdir.mkdir(exist_ok=True)
-    mgs_data = MGSData.from_repo()
+    mgs_data = MGSData.from_repo(ref=branch)
     input_data = []
     output_data = []
     for (